16-80407239-T-C

Variant names:

• chr16-80407239-T-C
• rs1126264
• ENST00000565050.5:n.598+83978A>G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000568776.5(DYNLRB2-AS1):​n.252+121403A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.727 in 151,984 control chromosomes in the GnomAD database, including 42,365 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.73 (42365 hom., cov: 30)
• Consequence: DYNLRB2-AS1 ENST00000568776.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.490

Genes affected

DYNLRB2-AS1 (HGNC:55405): (DYNLRB2 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.847 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DYNLRB2-AS1	NR_120307.1	n.252+121403A>G		intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DYNLRB2-AS1	ENST00000565050.5	n.598+83978A>G		intron_variant	Intron 3 of 4	5
DYNLRB2-AS1	ENST00000568776.5	n.252+121403A>G		intron_variant	Intron 2 of 5	4
DYNLRB2-AS1	ENST00000568819.5	n.362+85331A>G		intron_variant	Intron 3 of 4	5

Frequencies

GnomAD3 genomes AF: 0.727 AC: 110358 AN: 151866 Hom.: 42336 Cov.: 30

Gnomad AFR AF: 0.459

Gnomad AMI AF: 0.902

Gnomad AMR AF: 0.788

Gnomad ASJ AF: 0.706

Gnomad EAS AF: 0.760

Gnomad SAS AF: 0.763

Gnomad FIN AF: 0.828

Gnomad MID AF: 0.787

Gnomad NFE AF: 0.853

Gnomad OTH AF: 0.748

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.727 AC: 110431 AN: 151984 Hom.: 42365 Cov.: 30 AF XY: 0.728 AC XY: 54068 AN XY: 74302

Gnomad4 AFR AF: 0.459

Gnomad4 AMR AF: 0.788

Gnomad4 ASJ AF: 0.706

Gnomad4 EAS AF: 0.760

Gnomad4 SAS AF: 0.764

Gnomad4 FIN AF: 0.828

Gnomad4 NFE AF: 0.853

Gnomad4 OTH AF: 0.750

Alfa AF: 0.817 Hom.: 23526

Bravo AF: 0.712

Asia WGS AF: 0.761 AC: 2645 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.23
DANN	Benign	0.53

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1126264; hg19: chr16-80441136;